/*
#Copyright (c) 2013, Philippe Bordron <philippe.bordron@gmail.com>
#
# This file is part of SIPPER.
#
# DCC is free software: you can redistribute it and/or modify
# it under the terms of the GNU LESSER GENERAL PUBLIC LICENSE as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# DCC is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU LESSER GENERAL PUBLIC LICENSE for more details.
#
# You should have received a copy of the GNU LESSER GENERAL PUBLIC LICENSE
# along with SIPPER.  If not, see <http://www.gnu.org/licenses/>
*/
package combi.wip.sipper.modeling.metabolicNetwork.graphs;

import org.jgrapht.DirectedGraph;
import org.jgrapht.graph.DefaultDirectedGraph;
import org.jgrapht.graph.DefaultEdge;

import combi.wip.sipper.modeling.metabolicNetworks.MetabolicNetwork;
import combi.wip.sipper.modeling.reactions.Reaction;

public class ReactionGraph<C,R extends Reaction<C>> {

	private MetabolicNetwork<C,Reaction<C>> meta;
	
	public ReactionGraph(MetabolicNetwork<C,Reaction<C>> meta)
	{
		this.meta = meta;
	}
	
	public DirectedGraph<String, DefaultEdge> generateGraph()
	{
		DirectedGraph<String, DefaultEdge> result = new DefaultDirectedGraph<String, DefaultEdge>(DefaultEdge.class);
		for(Reaction<C> r : meta.getReactionSet())
		{
			result.addVertex(r.getId());
		}
		for(Reaction<C> src : meta.getReactionSet())
		{
			for(Reaction<C> dest : meta.nextReactions(src))
			{
				result.addEdge(src.getId(),dest.getId());
			}
		}
		return result;
	}
	
}
